Multiple sequence alignment - TraesCS6D01G075000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G075000 chr6D 100.000 5475 0 0 1 5475 38776978 38771504 0.000000e+00 10111
1 TraesCS6D01G075000 chr6D 98.575 842 12 0 4634 5475 16356609 16355768 0.000000e+00 1489
2 TraesCS6D01G075000 chr6D 98.575 842 12 0 4634 5475 363332797 363331956 0.000000e+00 1489
3 TraesCS6D01G075000 chr6D 98.456 842 13 0 4634 5475 82105302 82104461 0.000000e+00 1483
4 TraesCS6D01G075000 chr6D 98.456 842 13 0 4634 5475 296975966 296975125 0.000000e+00 1483
5 TraesCS6D01G075000 chr6D 97.479 119 3 0 605 723 38776223 38776105 2.590000e-48 204
6 TraesCS6D01G075000 chr6D 97.479 119 3 0 756 874 38776374 38776256 2.590000e-48 204
7 TraesCS6D01G075000 chr7A 97.285 3904 78 12 756 4634 617008323 617004423 0.000000e+00 6597
8 TraesCS6D01G075000 chr7A 92.690 684 37 7 3955 4634 104462260 104461586 0.000000e+00 974
9 TraesCS6D01G075000 chr7A 78.456 868 115 42 734 1542 108111161 108110307 8.190000e-138 501
10 TraesCS6D01G075000 chr7A 78.218 303 37 4 605 906 561606095 561606369 3.390000e-37 167
11 TraesCS6D01G075000 chr7A 90.000 120 12 0 604 723 561606218 561606337 7.340000e-34 156
12 TraesCS6D01G075000 chr5A 97.233 3903 83 12 754 4634 607949335 607953234 0.000000e+00 6586
13 TraesCS6D01G075000 chr5A 93.103 957 58 7 3127 4081 560600088 560599138 0.000000e+00 1395
14 TraesCS6D01G075000 chr5A 94.464 289 15 1 2845 3133 560600561 560600274 1.400000e-120 444
15 TraesCS6D01G075000 chr5A 84.979 466 35 17 2181 2615 560601261 560600800 1.810000e-119 440
16 TraesCS6D01G075000 chr5A 89.011 364 26 7 4273 4634 560598498 560598147 6.510000e-119 438
17 TraesCS6D01G075000 chr5A 77.679 784 94 43 739 1453 560602099 560601328 2.380000e-108 403
18 TraesCS6D01G075000 chr5A 89.916 119 12 0 605 723 607949337 607949455 2.640000e-33 154
19 TraesCS6D01G075000 chr5A 79.911 224 33 8 759 972 690942885 690942664 2.640000e-33 154
20 TraesCS6D01G075000 chr5A 89.831 118 12 0 606 723 492997664 492997547 9.500000e-33 152
21 TraesCS6D01G075000 chr3A 98.915 1382 15 0 3253 4634 694982242 694983623 0.000000e+00 2470
22 TraesCS6D01G075000 chr3A 90.670 1522 105 12 3127 4634 690721517 690723015 0.000000e+00 1989
23 TraesCS6D01G075000 chr3A 92.542 657 37 6 3955 4607 23890309 23890957 0.000000e+00 931
24 TraesCS6D01G075000 chr3A 88.016 751 64 10 1476 2212 485686830 485687568 0.000000e+00 865
25 TraesCS6D01G075000 chr3A 95.502 289 13 0 2845 3133 690720831 690721119 3.860000e-126 462
26 TraesCS6D01G075000 chr3A 84.120 466 28 20 2181 2615 690720136 690720586 5.100000e-110 409
27 TraesCS6D01G075000 chr3A 79.153 614 74 30 757 1330 690719287 690719886 5.180000e-100 375
28 TraesCS6D01G075000 chr3B 91.721 1522 95 13 3127 4634 277024980 277026484 0.000000e+00 2084
29 TraesCS6D01G075000 chr3B 91.059 1521 108 11 3127 4634 221134417 221132912 0.000000e+00 2030
30 TraesCS6D01G075000 chr3B 88.652 749 59 10 1476 2212 474408881 474409615 0.000000e+00 889
31 TraesCS6D01G075000 chr3B 85.622 466 34 12 2181 2615 277021758 277022221 5.000000e-125 459
32 TraesCS6D01G075000 chr3B 85.408 466 35 12 2181 2615 277019710 277020173 2.330000e-123 453
33 TraesCS6D01G075000 chr3B 85.193 466 36 12 2181 2615 277023802 277024265 1.080000e-121 448
34 TraesCS6D01G075000 chr3B 94.464 289 16 0 2845 3133 277020424 277020712 3.890000e-121 446
35 TraesCS6D01G075000 chr3B 94.464 289 16 0 2845 3133 277024506 277024794 3.890000e-121 446
36 TraesCS6D01G075000 chr3B 86.073 438 31 12 2181 2590 817346636 817346201 1.400000e-120 444
37 TraesCS6D01G075000 chr2B 91.460 1534 98 15 3127 4645 75906884 75908399 0.000000e+00 2076
38 TraesCS6D01G075000 chr2B 85.622 466 34 11 2181 2615 75905710 75906173 5.000000e-125 459
39 TraesCS6D01G075000 chr2B 94.464 289 16 0 2845 3133 75906410 75906698 3.890000e-121 446
40 TraesCS6D01G075000 chr2B 84.946 186 20 5 734 914 66032869 66033051 1.210000e-41 182
41 TraesCS6D01G075000 chr2B 84.768 151 18 5 733 883 760146852 760146707 4.420000e-31 147
42 TraesCS6D01G075000 chr1B 91.157 1538 101 16 3127 4648 123484350 123485868 0.000000e+00 2054
43 TraesCS6D01G075000 chr1B 84.120 466 41 12 2181 2615 123483171 123483634 2.360000e-113 420
44 TraesCS6D01G075000 chr1B 80.729 192 33 4 740 929 2438707 2438896 4.420000e-31 147
45 TraesCS6D01G075000 chr1B 88.430 121 14 0 603 723 55975965 55975845 4.420000e-31 147
46 TraesCS6D01G075000 chr2A 91.196 1522 97 12 3127 4634 721615690 721614192 0.000000e+00 2034
47 TraesCS6D01G075000 chr2A 93.275 684 33 7 3955 4634 543681104 543681778 0.000000e+00 996
48 TraesCS6D01G075000 chr2A 95.156 289 14 0 2845 3133 721616172 721615884 1.800000e-124 457
49 TraesCS6D01G075000 chr2A 84.335 466 27 20 2181 2615 721616866 721616416 1.100000e-111 414
50 TraesCS6D01G075000 chr2A 79.350 615 73 32 756 1330 721617716 721617116 3.090000e-102 383
51 TraesCS6D01G075000 chr2A 86.935 199 24 1 1344 1542 721617064 721616868 7.140000e-54 222
52 TraesCS6D01G075000 chr6A 90.550 1418 93 16 3232 4634 457042684 457041293 0.000000e+00 1838
53 TraesCS6D01G075000 chr6A 92.894 957 61 4 3127 4081 41601175 41602126 0.000000e+00 1384
54 TraesCS6D01G075000 chr6A 77.883 841 106 41 769 1542 41599175 41600002 3.010000e-122 449
55 TraesCS6D01G075000 chr6A 87.500 368 31 7 4273 4637 41602753 41603108 1.420000e-110 411
56 TraesCS6D01G075000 chr1D 91.796 1292 70 7 3127 4405 416150175 416151443 0.000000e+00 1766
57 TraesCS6D01G075000 chr1D 98.515 606 9 0 1 606 283637976 283637371 0.000000e+00 1070
58 TraesCS6D01G075000 chr1D 98.515 606 9 0 1 606 295172739 295173344 0.000000e+00 1070
59 TraesCS6D01G075000 chr1D 98.515 606 9 0 1 606 493883725 493884330 0.000000e+00 1070
60 TraesCS6D01G075000 chr1D 85.622 466 32 14 2181 2615 416149004 416149465 1.800000e-124 457
61 TraesCS6D01G075000 chr1D 94.810 289 15 0 2845 3133 416149701 416149989 8.360000e-123 451
62 TraesCS6D01G075000 chr1D 80.179 671 76 33 917 1542 416148344 416149002 3.010000e-122 449
63 TraesCS6D01G075000 chr7D 98.812 842 10 0 4634 5475 466129168 466130009 0.000000e+00 1500
64 TraesCS6D01G075000 chr7D 98.515 606 9 0 1 606 215110797 215110192 0.000000e+00 1070
65 TraesCS6D01G075000 chr3D 98.812 842 10 0 4634 5475 341373780 341372939 0.000000e+00 1500
66 TraesCS6D01G075000 chr3D 98.575 842 12 0 4634 5475 355397431 355398272 0.000000e+00 1489
67 TraesCS6D01G075000 chr3D 98.845 606 7 0 1 606 583432811 583433416 0.000000e+00 1081
68 TraesCS6D01G075000 chr3D 98.515 606 9 0 1 606 610494998 610494393 0.000000e+00 1070
69 TraesCS6D01G075000 chr3D 89.081 751 57 9 1476 2212 364263292 364264031 0.000000e+00 909
70 TraesCS6D01G075000 chr3D 88.235 119 14 0 605 723 18400450 18400332 5.720000e-30 143
71 TraesCS6D01G075000 chr3D 88.235 119 14 0 605 723 135860178 135860060 5.720000e-30 143
72 TraesCS6D01G075000 chr5D 98.694 842 11 0 4634 5475 228945496 228946337 0.000000e+00 1495
73 TraesCS6D01G075000 chr4D 98.694 842 11 0 4634 5475 20448917 20449758 0.000000e+00 1495
74 TraesCS6D01G075000 chr4D 98.350 606 10 0 1 606 459359939 459359334 0.000000e+00 1064
75 TraesCS6D01G075000 chr4D 90.083 121 12 0 603 723 490138358 490138238 2.040000e-34 158
76 TraesCS6D01G075000 chr2D 98.515 606 9 0 1 606 320136045 320135440 0.000000e+00 1070
77 TraesCS6D01G075000 chr2D 98.515 606 9 0 1 606 368495969 368496574 0.000000e+00 1070
78 TraesCS6D01G075000 chr2D 83.424 368 45 6 1809 2163 315108303 315108667 1.470000e-85 327
79 TraesCS6D01G075000 chr2D 80.576 417 52 9 1809 2212 612483385 612483785 1.490000e-75 294
80 TraesCS6D01G075000 chr2D 87.550 249 31 0 1476 1724 612483140 612483388 6.940000e-74 289
81 TraesCS6D01G075000 chrUn 98.458 389 5 1 2288 2675 480104604 480104992 0.000000e+00 684
82 TraesCS6D01G075000 chrUn 84.615 260 21 14 1077 1330 476699348 476699594 1.970000e-59 241
83 TraesCS6D01G075000 chr1A 82.536 418 43 11 1809 2212 97188182 97188583 1.890000e-89 340
84 TraesCS6D01G075000 chr1A 86.747 249 31 1 1476 1724 97187939 97188185 5.400000e-70 276
85 TraesCS6D01G075000 chr6B 84.795 171 21 5 757 924 22729515 22729683 3.390000e-37 167
86 TraesCS6D01G075000 chr7B 84.024 169 19 6 756 923 642772327 642772488 7.340000e-34 156


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G075000 chr6D 38771504 38776978 5474 True 3506.333333 10111 98.319333 1 5475 3 chr6D.!!$R5 5474
1 TraesCS6D01G075000 chr6D 16355768 16356609 841 True 1489.000000 1489 98.575000 4634 5475 1 chr6D.!!$R1 841
2 TraesCS6D01G075000 chr6D 363331956 363332797 841 True 1489.000000 1489 98.575000 4634 5475 1 chr6D.!!$R4 841
3 TraesCS6D01G075000 chr6D 82104461 82105302 841 True 1483.000000 1483 98.456000 4634 5475 1 chr6D.!!$R2 841
4 TraesCS6D01G075000 chr6D 296975125 296975966 841 True 1483.000000 1483 98.456000 4634 5475 1 chr6D.!!$R3 841
5 TraesCS6D01G075000 chr7A 617004423 617008323 3900 True 6597.000000 6597 97.285000 756 4634 1 chr7A.!!$R3 3878
6 TraesCS6D01G075000 chr7A 104461586 104462260 674 True 974.000000 974 92.690000 3955 4634 1 chr7A.!!$R1 679
7 TraesCS6D01G075000 chr7A 108110307 108111161 854 True 501.000000 501 78.456000 734 1542 1 chr7A.!!$R2 808
8 TraesCS6D01G075000 chr5A 607949335 607953234 3899 False 3370.000000 6586 93.574500 605 4634 2 chr5A.!!$F1 4029
9 TraesCS6D01G075000 chr5A 560598147 560602099 3952 True 624.000000 1395 87.847200 739 4634 5 chr5A.!!$R3 3895
10 TraesCS6D01G075000 chr3A 694982242 694983623 1381 False 2470.000000 2470 98.915000 3253 4634 1 chr3A.!!$F3 1381
11 TraesCS6D01G075000 chr3A 23890309 23890957 648 False 931.000000 931 92.542000 3955 4607 1 chr3A.!!$F1 652
12 TraesCS6D01G075000 chr3A 485686830 485687568 738 False 865.000000 865 88.016000 1476 2212 1 chr3A.!!$F2 736
13 TraesCS6D01G075000 chr3A 690719287 690723015 3728 False 808.750000 1989 87.361250 757 4634 4 chr3A.!!$F4 3877
14 TraesCS6D01G075000 chr3B 221132912 221134417 1505 True 2030.000000 2030 91.059000 3127 4634 1 chr3B.!!$R1 1507
15 TraesCS6D01G075000 chr3B 474408881 474409615 734 False 889.000000 889 88.652000 1476 2212 1 chr3B.!!$F1 736
16 TraesCS6D01G075000 chr3B 277019710 277026484 6774 False 722.666667 2084 89.478667 2181 4634 6 chr3B.!!$F2 2453
17 TraesCS6D01G075000 chr2B 75905710 75908399 2689 False 993.666667 2076 90.515333 2181 4645 3 chr2B.!!$F2 2464
18 TraesCS6D01G075000 chr1B 123483171 123485868 2697 False 1237.000000 2054 87.638500 2181 4648 2 chr1B.!!$F2 2467
19 TraesCS6D01G075000 chr2A 543681104 543681778 674 False 996.000000 996 93.275000 3955 4634 1 chr2A.!!$F1 679
20 TraesCS6D01G075000 chr2A 721614192 721617716 3524 True 702.000000 2034 87.394400 756 4634 5 chr2A.!!$R1 3878
21 TraesCS6D01G075000 chr6A 457041293 457042684 1391 True 1838.000000 1838 90.550000 3232 4634 1 chr6A.!!$R1 1402
22 TraesCS6D01G075000 chr6A 41599175 41603108 3933 False 748.000000 1384 86.092333 769 4637 3 chr6A.!!$F1 3868
23 TraesCS6D01G075000 chr1D 283637371 283637976 605 True 1070.000000 1070 98.515000 1 606 1 chr1D.!!$R1 605
24 TraesCS6D01G075000 chr1D 295172739 295173344 605 False 1070.000000 1070 98.515000 1 606 1 chr1D.!!$F1 605
25 TraesCS6D01G075000 chr1D 493883725 493884330 605 False 1070.000000 1070 98.515000 1 606 1 chr1D.!!$F2 605
26 TraesCS6D01G075000 chr1D 416148344 416151443 3099 False 780.750000 1766 88.101750 917 4405 4 chr1D.!!$F3 3488
27 TraesCS6D01G075000 chr7D 466129168 466130009 841 False 1500.000000 1500 98.812000 4634 5475 1 chr7D.!!$F1 841
28 TraesCS6D01G075000 chr7D 215110192 215110797 605 True 1070.000000 1070 98.515000 1 606 1 chr7D.!!$R1 605
29 TraesCS6D01G075000 chr3D 341372939 341373780 841 True 1500.000000 1500 98.812000 4634 5475 1 chr3D.!!$R3 841
30 TraesCS6D01G075000 chr3D 355397431 355398272 841 False 1489.000000 1489 98.575000 4634 5475 1 chr3D.!!$F1 841
31 TraesCS6D01G075000 chr3D 583432811 583433416 605 False 1081.000000 1081 98.845000 1 606 1 chr3D.!!$F3 605
32 TraesCS6D01G075000 chr3D 610494393 610494998 605 True 1070.000000 1070 98.515000 1 606 1 chr3D.!!$R4 605
33 TraesCS6D01G075000 chr3D 364263292 364264031 739 False 909.000000 909 89.081000 1476 2212 1 chr3D.!!$F2 736
34 TraesCS6D01G075000 chr5D 228945496 228946337 841 False 1495.000000 1495 98.694000 4634 5475 1 chr5D.!!$F1 841
35 TraesCS6D01G075000 chr4D 20448917 20449758 841 False 1495.000000 1495 98.694000 4634 5475 1 chr4D.!!$F1 841
36 TraesCS6D01G075000 chr4D 459359334 459359939 605 True 1064.000000 1064 98.350000 1 606 1 chr4D.!!$R1 605
37 TraesCS6D01G075000 chr2D 320135440 320136045 605 True 1070.000000 1070 98.515000 1 606 1 chr2D.!!$R1 605
38 TraesCS6D01G075000 chr2D 368495969 368496574 605 False 1070.000000 1070 98.515000 1 606 1 chr2D.!!$F2 605
39 TraesCS6D01G075000 chr2D 612483140 612483785 645 False 291.500000 294 84.063000 1476 2212 2 chr2D.!!$F3 736
40 TraesCS6D01G075000 chr1A 97187939 97188583 644 False 308.000000 340 84.641500 1476 2212 2 chr1A.!!$F1 736

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
693 694 0.033796 TCAGGACCCTCGGATTACGT 60.034 55.000 0.0 0.0 44.69 3.57 F
922 946 0.465705 TCTGGGATCAATCGTCTGCC 59.534 55.000 0.0 0.0 0.00 4.85 F
2741 7008 1.431440 GCGAGAGAGCGAGTCACAT 59.569 57.895 0.0 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2683 6919 0.650512 ACTCGACGCAACAAACACAG 59.349 50.000 0.0 0.0 0.00 3.66 R
2906 7222 1.271102 GCTCGCCCCAACAACAAATTA 59.729 47.619 0.0 0.0 0.00 1.40 R
4683 9875 0.951040 GACGGTGTCAAGAAGGGCAG 60.951 60.000 0.0 0.0 32.09 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 1.291272 GTCGCGGTCTTAGTGGGTT 59.709 57.895 6.13 0.00 0.00 4.11
347 348 2.047274 ACTCGACATTGGTGGGCG 60.047 61.111 0.00 0.00 0.00 6.13
519 520 6.235664 GGTCCTTTGATGTTAGTAACAAGGA 58.764 40.000 22.23 22.23 45.86 3.36
528 529 8.696374 TGATGTTAGTAACAAGGATCTTAGGAG 58.304 37.037 19.19 0.00 45.86 3.69
556 557 9.519191 CCAAATGGACCATTCAATATACTCATA 57.481 33.333 20.06 0.00 32.43 2.15
606 607 1.430632 CCATCACTTGCACGGCATC 59.569 57.895 0.00 0.00 38.76 3.91
607 608 1.028330 CCATCACTTGCACGGCATCT 61.028 55.000 0.00 0.00 38.76 2.90
608 609 1.655484 CATCACTTGCACGGCATCTA 58.345 50.000 0.00 0.00 38.76 1.98
609 610 2.216046 CATCACTTGCACGGCATCTAT 58.784 47.619 0.00 0.00 38.76 1.98
610 611 3.392882 CATCACTTGCACGGCATCTATA 58.607 45.455 0.00 0.00 38.76 1.31
611 612 2.821546 TCACTTGCACGGCATCTATAC 58.178 47.619 0.00 0.00 38.76 1.47
612 613 2.430694 TCACTTGCACGGCATCTATACT 59.569 45.455 0.00 0.00 38.76 2.12
613 614 3.634910 TCACTTGCACGGCATCTATACTA 59.365 43.478 0.00 0.00 38.76 1.82
614 615 3.736252 CACTTGCACGGCATCTATACTAC 59.264 47.826 0.00 0.00 38.76 2.73
615 616 3.637229 ACTTGCACGGCATCTATACTACT 59.363 43.478 0.00 0.00 38.76 2.57
616 617 4.825634 ACTTGCACGGCATCTATACTACTA 59.174 41.667 0.00 0.00 38.76 1.82
617 618 5.477291 ACTTGCACGGCATCTATACTACTAT 59.523 40.000 0.00 0.00 38.76 2.12
618 619 5.977489 TGCACGGCATCTATACTACTATT 57.023 39.130 0.00 0.00 31.71 1.73
619 620 7.176165 ACTTGCACGGCATCTATACTACTATTA 59.824 37.037 0.00 0.00 38.76 0.98
620 621 7.457024 TGCACGGCATCTATACTACTATTAA 57.543 36.000 0.00 0.00 31.71 1.40
621 622 7.888424 TGCACGGCATCTATACTACTATTAAA 58.112 34.615 0.00 0.00 31.71 1.52
622 623 8.361889 TGCACGGCATCTATACTACTATTAAAA 58.638 33.333 0.00 0.00 31.71 1.52
623 624 8.861101 GCACGGCATCTATACTACTATTAAAAG 58.139 37.037 0.00 0.00 0.00 2.27
626 627 9.291664 CGGCATCTATACTACTATTAAAAGAGC 57.708 37.037 0.00 0.00 0.00 4.09
646 647 9.612620 AAAGAGCAAACATAATTTCTTCTAACG 57.387 29.630 0.00 0.00 0.00 3.18
647 648 7.244192 AGAGCAAACATAATTTCTTCTAACGC 58.756 34.615 0.00 0.00 0.00 4.84
648 649 6.322491 AGCAAACATAATTTCTTCTAACGCC 58.678 36.000 0.00 0.00 0.00 5.68
649 650 6.072175 AGCAAACATAATTTCTTCTAACGCCA 60.072 34.615 0.00 0.00 0.00 5.69
650 651 6.033513 GCAAACATAATTTCTTCTAACGCCAC 59.966 38.462 0.00 0.00 0.00 5.01
651 652 6.811253 AACATAATTTCTTCTAACGCCACA 57.189 33.333 0.00 0.00 0.00 4.17
652 653 6.178239 ACATAATTTCTTCTAACGCCACAC 57.822 37.500 0.00 0.00 0.00 3.82
653 654 5.703592 ACATAATTTCTTCTAACGCCACACA 59.296 36.000 0.00 0.00 0.00 3.72
654 655 6.205853 ACATAATTTCTTCTAACGCCACACAA 59.794 34.615 0.00 0.00 0.00 3.33
655 656 3.955771 TTTCTTCTAACGCCACACAAC 57.044 42.857 0.00 0.00 0.00 3.32
656 657 2.605837 TCTTCTAACGCCACACAACA 57.394 45.000 0.00 0.00 0.00 3.33
657 658 2.907634 TCTTCTAACGCCACACAACAA 58.092 42.857 0.00 0.00 0.00 2.83
658 659 3.271729 TCTTCTAACGCCACACAACAAA 58.728 40.909 0.00 0.00 0.00 2.83
659 660 3.064271 TCTTCTAACGCCACACAACAAAC 59.936 43.478 0.00 0.00 0.00 2.93
660 661 2.634600 TCTAACGCCACACAACAAACT 58.365 42.857 0.00 0.00 0.00 2.66
661 662 3.794717 TCTAACGCCACACAACAAACTA 58.205 40.909 0.00 0.00 0.00 2.24
662 663 4.382291 TCTAACGCCACACAACAAACTAT 58.618 39.130 0.00 0.00 0.00 2.12
663 664 5.539979 TCTAACGCCACACAACAAACTATA 58.460 37.500 0.00 0.00 0.00 1.31
664 665 4.477302 AACGCCACACAACAAACTATAC 57.523 40.909 0.00 0.00 0.00 1.47
665 666 3.468770 ACGCCACACAACAAACTATACA 58.531 40.909 0.00 0.00 0.00 2.29
666 667 3.249080 ACGCCACACAACAAACTATACAC 59.751 43.478 0.00 0.00 0.00 2.90
667 668 3.496884 CGCCACACAACAAACTATACACT 59.503 43.478 0.00 0.00 0.00 3.55
668 669 4.610456 CGCCACACAACAAACTATACACTG 60.610 45.833 0.00 0.00 0.00 3.66
669 670 4.320202 GCCACACAACAAACTATACACTGG 60.320 45.833 0.00 0.00 0.00 4.00
670 671 5.060506 CCACACAACAAACTATACACTGGA 58.939 41.667 0.00 0.00 0.00 3.86
671 672 5.705441 CCACACAACAAACTATACACTGGAT 59.295 40.000 0.00 0.00 0.00 3.41
672 673 6.876789 CCACACAACAAACTATACACTGGATA 59.123 38.462 0.00 0.00 0.00 2.59
673 674 7.389330 CCACACAACAAACTATACACTGGATAA 59.611 37.037 0.00 0.00 0.00 1.75
674 675 8.946085 CACACAACAAACTATACACTGGATAAT 58.054 33.333 0.00 0.00 0.00 1.28
675 676 9.162764 ACACAACAAACTATACACTGGATAATC 57.837 33.333 0.00 0.00 0.00 1.75
676 677 9.161629 CACAACAAACTATACACTGGATAATCA 57.838 33.333 0.00 0.00 0.00 2.57
677 678 9.383519 ACAACAAACTATACACTGGATAATCAG 57.616 33.333 0.00 0.00 40.40 2.90
678 679 8.830580 CAACAAACTATACACTGGATAATCAGG 58.169 37.037 0.00 0.00 38.98 3.86
679 680 8.319057 ACAAACTATACACTGGATAATCAGGA 57.681 34.615 0.00 0.00 38.98 3.86
680 681 8.204836 ACAAACTATACACTGGATAATCAGGAC 58.795 37.037 0.00 0.00 38.98 3.85
681 682 6.919775 ACTATACACTGGATAATCAGGACC 57.080 41.667 0.00 0.00 38.98 4.46
682 683 5.780793 ACTATACACTGGATAATCAGGACCC 59.219 44.000 0.00 0.00 38.98 4.46
683 684 3.136641 ACACTGGATAATCAGGACCCT 57.863 47.619 0.00 0.00 38.98 4.34
684 685 3.041946 ACACTGGATAATCAGGACCCTC 58.958 50.000 0.00 0.00 38.98 4.30
685 686 2.036475 CACTGGATAATCAGGACCCTCG 59.964 54.545 0.00 0.00 38.98 4.63
686 687 1.620819 CTGGATAATCAGGACCCTCGG 59.379 57.143 0.00 0.00 0.00 4.63
687 688 1.219469 TGGATAATCAGGACCCTCGGA 59.781 52.381 0.00 0.00 0.00 4.55
688 689 2.158158 TGGATAATCAGGACCCTCGGAT 60.158 50.000 0.00 0.00 0.00 4.18
689 690 2.907042 GGATAATCAGGACCCTCGGATT 59.093 50.000 6.79 6.79 34.58 3.01
690 691 4.094476 GGATAATCAGGACCCTCGGATTA 58.906 47.826 9.76 9.76 36.85 1.75
691 692 4.081586 GGATAATCAGGACCCTCGGATTAC 60.082 50.000 9.62 5.99 35.68 1.89
692 693 1.329256 ATCAGGACCCTCGGATTACG 58.671 55.000 0.00 0.00 46.11 3.18
693 694 0.033796 TCAGGACCCTCGGATTACGT 60.034 55.000 0.00 0.00 44.69 3.57
694 695 0.822164 CAGGACCCTCGGATTACGTT 59.178 55.000 0.00 0.00 44.69 3.99
695 696 2.026641 CAGGACCCTCGGATTACGTTA 58.973 52.381 0.00 0.00 44.69 3.18
696 697 2.428171 CAGGACCCTCGGATTACGTTAA 59.572 50.000 0.00 0.00 44.69 2.01
697 698 2.428530 AGGACCCTCGGATTACGTTAAC 59.571 50.000 0.00 0.00 44.69 2.01
698 699 2.428530 GGACCCTCGGATTACGTTAACT 59.571 50.000 3.71 0.00 44.69 2.24
699 700 3.118992 GGACCCTCGGATTACGTTAACTT 60.119 47.826 3.71 0.00 44.69 2.66
700 701 4.097892 GGACCCTCGGATTACGTTAACTTA 59.902 45.833 3.71 0.00 44.69 2.24
701 702 5.394115 GGACCCTCGGATTACGTTAACTTAA 60.394 44.000 6.97 6.97 44.69 1.85
702 703 6.036577 ACCCTCGGATTACGTTAACTTAAA 57.963 37.500 8.44 0.00 44.69 1.52
703 704 5.869344 ACCCTCGGATTACGTTAACTTAAAC 59.131 40.000 8.44 6.19 44.69 2.01
704 705 5.868801 CCCTCGGATTACGTTAACTTAAACA 59.131 40.000 8.44 0.00 44.69 2.83
705 706 6.536224 CCCTCGGATTACGTTAACTTAAACAT 59.464 38.462 8.44 0.00 44.69 2.71
706 707 7.706179 CCCTCGGATTACGTTAACTTAAACATA 59.294 37.037 8.44 0.00 44.69 2.29
707 708 9.252962 CCTCGGATTACGTTAACTTAAACATAT 57.747 33.333 8.44 0.00 44.69 1.78
709 710 9.248291 TCGGATTACGTTAACTTAAACATATCC 57.752 33.333 8.44 9.17 44.69 2.59
710 711 9.252962 CGGATTACGTTAACTTAAACATATCCT 57.747 33.333 8.44 0.00 37.93 3.24
716 717 9.578439 ACGTTAACTTAAACATATCCTACTGTC 57.422 33.333 3.71 0.00 0.00 3.51
717 718 9.028185 CGTTAACTTAAACATATCCTACTGTCC 57.972 37.037 3.71 0.00 0.00 4.02
718 719 9.880157 GTTAACTTAAACATATCCTACTGTCCA 57.120 33.333 0.00 0.00 0.00 4.02
842 844 4.081586 GGATAATCAGGACCCTCGGATTAC 60.082 50.000 9.62 5.99 35.68 1.89
845 847 0.822164 CAGGACCCTCGGATTACGTT 59.178 55.000 0.00 0.00 44.69 3.99
915 917 3.806521 CAGATCAACGTCTGGGATCAATC 59.193 47.826 16.62 5.22 41.49 2.67
922 946 0.465705 TCTGGGATCAATCGTCTGCC 59.534 55.000 0.00 0.00 0.00 4.85
1239 1275 2.986979 TACCGGCGCAGTCTGACA 60.987 61.111 10.83 0.00 0.00 3.58
1406 1481 4.760715 TCTAGGAATACCGTCTCTGCATAC 59.239 45.833 0.00 0.00 41.83 2.39
2374 2491 8.112822 TGGTGGATTTTATATTTCTCAGGTCAA 58.887 33.333 0.00 0.00 0.00 3.18
2380 2497 7.605410 TTTATATTTCTCAGGTCAAACGGTC 57.395 36.000 0.00 0.00 0.00 4.79
2683 6919 7.127042 ACTCGATCGAATCTAATCGTATATGC 58.873 38.462 19.92 0.00 43.91 3.14
2741 7008 1.431440 GCGAGAGAGCGAGTCACAT 59.569 57.895 0.00 0.00 0.00 3.21
2833 7100 7.616313 ACTTAAAGTCGATCTTGATTTCCTCT 58.384 34.615 0.00 0.00 36.40 3.69
2906 7222 4.584743 GTGTGGGATCCTTTTTCTGTTCTT 59.415 41.667 12.58 0.00 0.00 2.52
4683 9875 2.167662 CTTTGTTGGATGGGGTGGTAC 58.832 52.381 0.00 0.00 0.00 3.34
4899 10091 4.593206 TGAGGTTCTTCTCACCTTGTATGT 59.407 41.667 0.00 0.00 45.30 2.29
5166 10358 1.128200 AACCCCAAGTTTTGCCTTCC 58.872 50.000 0.00 0.00 33.89 3.46
5169 10361 0.825840 CCCAAGTTTTGCCTTCCCGA 60.826 55.000 0.00 0.00 0.00 5.14
5187 10379 1.719780 CGAAGTTTAGCACACGAGACC 59.280 52.381 0.00 0.00 31.82 3.85
5453 10645 7.466804 TGAGTTTACCCATAAAGGTCTCAAAT 58.533 34.615 0.00 0.00 41.58 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 6.403049 TCTATGTGATTAACTTTTCGGAGCA 58.597 36.000 0.00 0.00 0.00 4.26
347 348 3.262420 ACGTGCACAAGATTCCATCTAC 58.738 45.455 18.64 0.00 39.08 2.59
519 520 2.175715 GGTCCATTTGGGCTCCTAAGAT 59.824 50.000 0.54 0.00 40.38 2.40
528 529 4.961438 ATATTGAATGGTCCATTTGGGC 57.039 40.909 18.31 6.33 39.63 5.36
556 557 5.096443 TGCCAAATTTGTTGGTTCTCTTT 57.904 34.783 16.73 0.00 41.53 2.52
558 559 4.961438 ATGCCAAATTTGTTGGTTCTCT 57.039 36.364 16.73 0.00 41.53 3.10
620 621 9.612620 CGTTAGAAGAAATTATGTTTGCTCTTT 57.387 29.630 0.00 0.00 0.00 2.52
621 622 7.750903 GCGTTAGAAGAAATTATGTTTGCTCTT 59.249 33.333 0.00 0.00 0.00 2.85
622 623 7.244192 GCGTTAGAAGAAATTATGTTTGCTCT 58.756 34.615 0.00 0.00 0.00 4.09
623 624 6.469275 GGCGTTAGAAGAAATTATGTTTGCTC 59.531 38.462 0.00 0.00 0.00 4.26
624 625 6.072175 TGGCGTTAGAAGAAATTATGTTTGCT 60.072 34.615 0.00 0.00 0.00 3.91
625 626 6.033513 GTGGCGTTAGAAGAAATTATGTTTGC 59.966 38.462 0.00 0.00 0.00 3.68
626 627 7.060633 GTGTGGCGTTAGAAGAAATTATGTTTG 59.939 37.037 0.00 0.00 0.00 2.93
627 628 7.081976 GTGTGGCGTTAGAAGAAATTATGTTT 58.918 34.615 0.00 0.00 0.00 2.83
628 629 6.205853 TGTGTGGCGTTAGAAGAAATTATGTT 59.794 34.615 0.00 0.00 0.00 2.71
629 630 5.703592 TGTGTGGCGTTAGAAGAAATTATGT 59.296 36.000 0.00 0.00 0.00 2.29
630 631 6.176975 TGTGTGGCGTTAGAAGAAATTATG 57.823 37.500 0.00 0.00 0.00 1.90
631 632 6.205853 TGTTGTGTGGCGTTAGAAGAAATTAT 59.794 34.615 0.00 0.00 0.00 1.28
632 633 5.527951 TGTTGTGTGGCGTTAGAAGAAATTA 59.472 36.000 0.00 0.00 0.00 1.40
633 634 4.336993 TGTTGTGTGGCGTTAGAAGAAATT 59.663 37.500 0.00 0.00 0.00 1.82
634 635 3.880490 TGTTGTGTGGCGTTAGAAGAAAT 59.120 39.130 0.00 0.00 0.00 2.17
635 636 3.271729 TGTTGTGTGGCGTTAGAAGAAA 58.728 40.909 0.00 0.00 0.00 2.52
636 637 2.907634 TGTTGTGTGGCGTTAGAAGAA 58.092 42.857 0.00 0.00 0.00 2.52
637 638 2.605837 TGTTGTGTGGCGTTAGAAGA 57.394 45.000 0.00 0.00 0.00 2.87
638 639 3.064820 AGTTTGTTGTGTGGCGTTAGAAG 59.935 43.478 0.00 0.00 0.00 2.85
639 640 3.011119 AGTTTGTTGTGTGGCGTTAGAA 58.989 40.909 0.00 0.00 0.00 2.10
640 641 2.634600 AGTTTGTTGTGTGGCGTTAGA 58.365 42.857 0.00 0.00 0.00 2.10
641 642 4.742438 ATAGTTTGTTGTGTGGCGTTAG 57.258 40.909 0.00 0.00 0.00 2.34
642 643 5.050227 GTGTATAGTTTGTTGTGTGGCGTTA 60.050 40.000 0.00 0.00 0.00 3.18
643 644 3.878103 TGTATAGTTTGTTGTGTGGCGTT 59.122 39.130 0.00 0.00 0.00 4.84
644 645 3.249080 GTGTATAGTTTGTTGTGTGGCGT 59.751 43.478 0.00 0.00 0.00 5.68
645 646 3.496884 AGTGTATAGTTTGTTGTGTGGCG 59.503 43.478 0.00 0.00 0.00 5.69
646 647 4.320202 CCAGTGTATAGTTTGTTGTGTGGC 60.320 45.833 0.00 0.00 0.00 5.01
647 648 5.060506 TCCAGTGTATAGTTTGTTGTGTGG 58.939 41.667 0.00 0.00 0.00 4.17
648 649 6.801539 ATCCAGTGTATAGTTTGTTGTGTG 57.198 37.500 0.00 0.00 0.00 3.82
649 650 9.162764 GATTATCCAGTGTATAGTTTGTTGTGT 57.837 33.333 0.00 0.00 0.00 3.72
650 651 9.161629 TGATTATCCAGTGTATAGTTTGTTGTG 57.838 33.333 0.00 0.00 0.00 3.33
651 652 9.383519 CTGATTATCCAGTGTATAGTTTGTTGT 57.616 33.333 0.00 0.00 0.00 3.32
652 653 8.830580 CCTGATTATCCAGTGTATAGTTTGTTG 58.169 37.037 0.00 0.00 32.43 3.33
653 654 8.768397 TCCTGATTATCCAGTGTATAGTTTGTT 58.232 33.333 0.00 0.00 32.43 2.83
654 655 8.204836 GTCCTGATTATCCAGTGTATAGTTTGT 58.795 37.037 0.00 0.00 32.43 2.83
655 656 7.657761 GGTCCTGATTATCCAGTGTATAGTTTG 59.342 40.741 0.00 0.00 32.43 2.93
656 657 7.202102 GGGTCCTGATTATCCAGTGTATAGTTT 60.202 40.741 0.00 0.00 32.43 2.66
657 658 6.270231 GGGTCCTGATTATCCAGTGTATAGTT 59.730 42.308 0.00 0.00 32.43 2.24
658 659 5.780793 GGGTCCTGATTATCCAGTGTATAGT 59.219 44.000 0.00 0.00 32.43 2.12
659 660 6.019748 AGGGTCCTGATTATCCAGTGTATAG 58.980 44.000 0.00 0.00 32.43 1.31
660 661 5.977533 AGGGTCCTGATTATCCAGTGTATA 58.022 41.667 0.00 0.00 32.43 1.47
661 662 4.832492 AGGGTCCTGATTATCCAGTGTAT 58.168 43.478 0.00 0.00 32.43 2.29
662 663 4.223953 GAGGGTCCTGATTATCCAGTGTA 58.776 47.826 0.00 0.00 32.43 2.90
663 664 3.041946 GAGGGTCCTGATTATCCAGTGT 58.958 50.000 0.00 0.00 32.43 3.55
664 665 2.036475 CGAGGGTCCTGATTATCCAGTG 59.964 54.545 0.00 0.00 32.43 3.66
665 666 2.320781 CGAGGGTCCTGATTATCCAGT 58.679 52.381 0.00 0.00 32.43 4.00
666 667 1.620819 CCGAGGGTCCTGATTATCCAG 59.379 57.143 0.00 0.00 0.00 3.86
667 668 1.219469 TCCGAGGGTCCTGATTATCCA 59.781 52.381 0.00 0.00 0.00 3.41
668 669 2.011122 TCCGAGGGTCCTGATTATCC 57.989 55.000 0.00 0.00 0.00 2.59
669 670 4.380655 CGTAATCCGAGGGTCCTGATTATC 60.381 50.000 10.86 0.00 39.56 1.75
670 671 3.510360 CGTAATCCGAGGGTCCTGATTAT 59.490 47.826 10.86 0.00 39.56 1.28
671 672 2.889045 CGTAATCCGAGGGTCCTGATTA 59.111 50.000 0.00 0.44 39.56 1.75
672 673 1.687123 CGTAATCCGAGGGTCCTGATT 59.313 52.381 0.00 1.38 39.56 2.57
673 674 1.329256 CGTAATCCGAGGGTCCTGAT 58.671 55.000 0.00 0.00 39.56 2.90
674 675 0.033796 ACGTAATCCGAGGGTCCTGA 60.034 55.000 0.00 0.00 40.70 3.86
675 676 0.822164 AACGTAATCCGAGGGTCCTG 59.178 55.000 0.00 0.00 40.70 3.86
676 677 2.428530 GTTAACGTAATCCGAGGGTCCT 59.571 50.000 0.00 0.00 40.70 3.85
677 678 2.428530 AGTTAACGTAATCCGAGGGTCC 59.571 50.000 0.00 0.00 40.70 4.46
678 679 3.790152 AGTTAACGTAATCCGAGGGTC 57.210 47.619 0.00 0.00 40.70 4.46
679 680 5.659440 TTAAGTTAACGTAATCCGAGGGT 57.341 39.130 9.55 0.00 40.70 4.34
680 681 5.868801 TGTTTAAGTTAACGTAATCCGAGGG 59.131 40.000 13.61 0.00 40.70 4.30
681 682 6.949578 TGTTTAAGTTAACGTAATCCGAGG 57.050 37.500 13.61 0.00 40.70 4.63
683 684 9.248291 GGATATGTTTAAGTTAACGTAATCCGA 57.752 33.333 13.61 5.65 40.70 4.55
684 685 9.252962 AGGATATGTTTAAGTTAACGTAATCCG 57.747 33.333 13.61 0.00 44.03 4.18
690 691 9.578439 GACAGTAGGATATGTTTAAGTTAACGT 57.422 33.333 0.00 0.00 0.00 3.99
691 692 9.028185 GGACAGTAGGATATGTTTAAGTTAACG 57.972 37.037 0.00 0.00 0.00 3.18
692 693 9.880157 TGGACAGTAGGATATGTTTAAGTTAAC 57.120 33.333 0.00 0.00 0.00 2.01
787 789 1.139256 TGTTGTGTGGCGTTAGGAGAA 59.861 47.619 0.00 0.00 0.00 2.87
842 844 9.028185 GGACAGTAGGATATGTTTAAGTTAACG 57.972 37.037 0.00 0.00 0.00 3.18
915 917 4.077184 TAGGGCGGTTGGCAGACG 62.077 66.667 8.30 8.30 46.16 4.18
1027 1053 1.205055 AAGAAGGATCGGGGAGGAAC 58.795 55.000 0.00 0.00 0.00 3.62
1320 1395 2.434359 GCACACGGGCAGAGGTAC 60.434 66.667 0.00 0.00 0.00 3.34
1667 1744 5.127682 GCCTGGGATTTACATTTGTCAGAAT 59.872 40.000 0.00 0.00 0.00 2.40
1874 1952 4.964897 TGAAATGCCCTCTAGATGAAGAGA 59.035 41.667 2.47 0.00 44.93 3.10
2374 2491 2.591715 GTGTGGCTGCAGACCGTT 60.592 61.111 19.23 0.00 0.00 4.44
2683 6919 0.650512 ACTCGACGCAACAAACACAG 59.349 50.000 0.00 0.00 0.00 3.66
2741 7008 8.702438 GTTATATAATAACAGGTAAAAGCGCGA 58.298 33.333 12.10 0.00 0.00 5.87
2833 7100 1.302949 GCCCTCATACAGGTGGCAA 59.697 57.895 0.00 0.00 41.51 4.52
2882 7198 2.504367 ACAGAAAAAGGATCCCACACG 58.496 47.619 8.55 0.00 0.00 4.49
2906 7222 1.271102 GCTCGCCCCAACAACAAATTA 59.729 47.619 0.00 0.00 0.00 1.40
3332 8052 3.462483 TGCTGGTAGTTCTCGTTTTCA 57.538 42.857 0.00 0.00 0.00 2.69
4683 9875 0.951040 GACGGTGTCAAGAAGGGCAG 60.951 60.000 0.00 0.00 32.09 4.85
4832 10024 1.360393 AAGTTGTGGCCAAGGAGGGA 61.360 55.000 7.24 0.00 38.09 4.20
4899 10091 4.202461 ACTTGAGAAAGGCCTTGTGTCATA 60.202 41.667 21.33 11.32 0.00 2.15
5166 10358 1.719780 GTCTCGTGTGCTAAACTTCGG 59.280 52.381 0.00 0.00 0.00 4.30
5169 10361 1.414919 TGGGTCTCGTGTGCTAAACTT 59.585 47.619 0.00 0.00 0.00 2.66
5187 10379 4.882427 AGATCTTGATCATGCTCTTGTTGG 59.118 41.667 12.44 0.00 0.00 3.77
5254 10446 1.204312 GAGCGTGGTCTTCGTTTGC 59.796 57.895 0.00 0.00 0.00 3.68


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.